breseq  version 0.30.0  revision f53f5bf51c1f
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Read File Information

read filereadsbasespassed filtersaveragelongestmapped
errorsqtrim-Atp-I-to-C-KO-15-134_S19_L001_R2_0012,191,310607,602,504100.0%277.3 bases301 bases93.4%
errorsqtrim-Atp-I-to-C-KO-15-134_S19_L001_R1_0012,191,387612,495,153100.0%279.5 bases301 bases99.3%
total4,382,6971,220,097,657100.0%278.4 bases301 bases96.4%

Reference Sequence Information

seq idlengthfit meanfit dispersion% mapped readsdescription
coveragedistributionNC_0009134,638,902267.57.7100.0%Escherichia coli str. K-12 substr. MG1655, complete genome.
total4,638,902100.0%

fit dispersion is the ratio of the variance to the mean for the negative binomial fit. It is =1 for Poisson and >1 for over-dispersed data.

New Junction Evidence

Junction Candidates Tested

optionlimitactual
Number of alignment pairs examined for constructing junction candidates≤ 1000005345
Coverage evenness (position-hash) score of junction candidates≥ 2≥ 2
Test this many junction candidates (n). May be smaller if not enough passed the coverage evenness threshold100 ≤ n ≤ 5000419
Total length of all junction candidates (factor times the reference genome length)≤ 0.10.055

Junction Skew Score Calculation

reference sequencepr(no read start)
NC_0009130.75033

pr(no read start) is the probability that there will not be an aligned read whose first base matches a given position on a given strand.

Final Junction Predictions

optionvalue
Coverage evenness (position-hash) score of predicted junctions must be≥ 3
Skew score of predicted junction (−log10 probability of unusual coverage evenness) must be≤ 3
Number of bases that at least one read must overlap each uniquely aligned side of a predicted junction≥ 1

Read Alignment Evidence

optionvalue
ModeConsensus/Mixed Base
Ploidy1 (haploid)
Consensus mutation E-value cutoff10
Consensus frequency cutoff0.8
Consensus minimum coverage each strandOFF
Polymorphism E-value cutoff10
Polymorphism frequency cutoff0.2
Polymorphism minimum coverage each strandOFF
Polymorphism bias cutoffOFF
Predict indel polymorphismsYES
Skip indel polymorphisms in homopolymers runs ofOFF
Skip base substitutions when they create a homopolymer flanked on each side byOFF

Software Versions

programversion
bowtie22.2.6
R3.3.1

Execution Times

stepstartendelapsed
Read and reference sequence file input22:42:57 24 Apr 201722:44:33 24 Apr 20171 minute 36 seconds
Read alignment to reference genome22:44:34 24 Apr 201722:51:59 24 Apr 20177 minutes 25 seconds
Preprocessing alignments for candidate junction identification22:51:59 24 Apr 201722:54:55 24 Apr 20172 minutes 56 seconds
Preliminary analysis of coverage distribution22:54:55 24 Apr 201722:59:15 24 Apr 20174 minutes 20 seconds
Identifying junction candidates22:59:15 24 Apr 201722:59:36 24 Apr 201721 seconds
Re-alignment to junction candidates22:59:36 24 Apr 201723:00:58 24 Apr 20171 minute 22 seconds
Resolving alignments with junction candidates23:00:58 24 Apr 201723:05:54 24 Apr 20174 minutes 56 seconds
Creating BAM files23:05:54 24 Apr 201723:08:12 24 Apr 20172 minutes 18 seconds
Tabulating error counts23:08:12 24 Apr 201723:13:38 24 Apr 20175 minutes 26 seconds
Re-calibrating base error rates23:13:38 24 Apr 201723:13:39 24 Apr 20171 second
Examining read alignment evidence23:13:39 24 Apr 201723:55:19 24 Apr 201741 minutes 40 seconds
Polymorphism statistics23:55:19 24 Apr 201723:55:19 24 Apr 20170 seconds
Output23:55:19 24 Apr 201723:55:52 24 Apr 201733 seconds
Total 1 hour 12 minutes 54 seconds